Complete example

gregorgorjanc · gregorgorjanc · commit 73b3d004b46b · 2026-01-27T22:55:15.000Z
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,3 +1,4 @@
-^RcppTskitTestPkgLinkingTo\.Rproj$
+^RcppTskitTestLinking\.Rproj$
 ^\.Rproj\.user$
+^\.github$
 ^LICENSE\.md$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,49 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, devel]
+  pull_request:
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - { os: macos-latest, r: "release" }
+          - { os: windows-latest, r: "release" }
+          - { os: ubuntu-latest, r: "release" }
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.gitignore b/.gitignore
@@ -5,3 +5,11 @@
 .httr-oauth
 .DS_Store
 .quarto
+src/Makevars
+src/Makevars.in
+.gitignore
+src/RcppTskitTestLinking.so
+src/test.o
+.gitignore
+src/Makevars.in
+src/RcppExports.o
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,13 +1,19 @@
-Package: RcppTskitTestPkgLinkingTo
+Package: RcppTskitTestLinking
 Title: Testing linking to and importing from RcppTskit
 Version: 0.1.0
 Authors@R:
     person("Gregor", "Gorjanc", , "gregor.gorjanc@gmail.com", role = c("aut", "cre", "cph"))
-Description: This is a stub package that shows how to link to and import
+Description: This is a demo package that shows how to link to and import
     from RcppTskit package, which provides R access to tskit C API.
 License: MIT + file LICENSE
+Depends:
+    R (>= 4.0.0)
+Imports:
+    methods,
+    RcppTskit (>= 0.1.0)
 LinkingTo:
-    RcppTskit
+    Rcpp (>= 0.12.10),
+    RcppTskit (>= 0.1.0)
 Remotes:
     git::git@bitbucket.org:HighlanderLab/RcppTskit.git?subdir=RcppTskit
 Encoding: UTF-8
diff --git a/LICENSE b/LICENSE
@@ -1,2 +1,2 @@
 YEAR: 2026
-COPYRIGHT HOLDER: RcppTskitTestPkgLinkingTo authors
+COPYRIGHT HOLDER: Gregor Gorjanc
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,2 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(ts_num_individuals_ptr2)
+import(RcppTskit)
+importFrom(methods,is)
+useDynLib(RcppTskitTestLinking, .registration = TRUE)
diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -0,0 +1,16 @@
+# Generated by using Rcpp::compileAttributes() -> do not edit by hand
+# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+#' @title Get number of individuals in tree sequence
+#' @param ts an external pointer to a \code{tsk_treeseq_t} object.
+#' @return integer number of individuals.
+#' @examples
+#' ts_file <- system.file("examples", "test.trees", package = "RcppTskit")
+#' ts <- RcppTskit::ts_load(ts_file)
+#' ts$num_individuals()
+#' ts_num_individuals_ptr2(ts$pointer)
+#' @export
+ts_num_individuals_ptr2 <- function(ts) {
+    .Call(`_RcppTskitTestLinking_ts_num_individuals_ptr2`, ts)
+}
+
diff --git a/R/RcppTskitTestLinkingTo-package.R b/R/RcppTskitTestLinkingTo-package.R
@@ -0,0 +1,9 @@
+#' @description
+#' This is a demo package that shows how to link to and import from RcppTskit
+#' package, which provides R access to tskit C API.
+#' @keywords internal
+#'
+#' @useDynLib RcppTskitTestLinking, .registration = TRUE
+#' @importFrom methods is
+#' @import RcppTskit
+"_PACKAGE"
diff --git a/README.md b/README.md
@@ -1,22 +1,33 @@
 
-# RcppTskitTestPkgLinkingTo
+# RcppTskitTestLinking
 
-The goal of RcppTskitTestPkgLinkingTo is to demonstrate
-how to link to and import from RcppTskit package,
-which provides R access to tskit C API.
+This is a demo package that shows how to link to and import from RcppTskit
+package, which provides R access to tskit C API.
 
-## Installation
+## Key files
 
-You can install the development version of RcppTskitTestPkgLinkingTo like so:
+The key files you should study are:
 
-``` r
-TODO
-```
+- `DESCRIPTION`
 
-## Example
+- `R/RcppTskitTestLinking-package.R`
 
-``` r
-library(RcppTskitTestPkgLinkingTo)
-TODO
-```
+- `src/test.cpp`
+
+- `src/Makevars.in` and `src/Makevars.win.in`
+
+- `tools/configure.R`
+
+- `configure` and `configure.win`
 
+- `cleanup` and `cleanup.win`
+
+## Install and test
+
+You can install and test this package by running:
+
+```
+remotes::install_github("HighlanderLab/RcppTskitTestLinking")
+library(RcppTskitTestLinking)
+?ts_num_individuals2
+```
diff --git a/RcppTskitTestLinking.Rproj b/RcppTskitTestLinking.Rproj
diff --git a/cleanup b/cleanup
@@ -0,0 +1,7 @@
+#!/bin/sh
+
+# Removing Makevars autogenerated via configure from src/Makevars.in
+rm -f src/Makevars
+
+# Removing compilation files
+rm -f src/*.o src/*.so
diff --git a/cleanup.win b/cleanup.win
@@ -0,0 +1,8 @@
+#!/bin/sh
+
+# Removing Makevars autogenerated via configure from src/Makevars.win.in
+rm -f src/Makevars.win
+
+# Removing compilation files
+# rm -f src/*.dll
+# TODO: check what is really needed! rm -f src/*.o src/*.so
diff --git a/configure b/configure
@@ -0,0 +1,2 @@
+#!/bin/sh
+"${R_HOME}/bin/Rscript" tools/configure.R
diff --git a/configure.win b/configure.win
@@ -0,0 +1,2 @@
+#!/bin/sh
+"${R_HOME}/${R_ARCH_BIN}/Rscript" tools/configure.R
diff --git a/man/RcppTskitTestLinking-package.Rd b/man/RcppTskitTestLinking-package.Rd
diff --git a/man/ts_num_individuals_ptr2.Rd b/man/ts_num_individuals_ptr2.Rd
diff --git a/notes.R b/notes.R
diff --git a/src/Makevars.in b/src/Makevars.in
@@ -1 +1 @@
-PKG_LIB = @RCPPTSKIT_LIB@
+PKG_LIBS = @RCPPTSKIT_LIB@
diff --git a/src/Makevars.win.in b/src/Makevars.win.in
@@ -0,0 +1 @@
+PKG_LIBS = @RCPPTSKIT_LIB@
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
@@ -0,0 +1,33 @@
+// Generated by using Rcpp::compileAttributes() -> do not edit by hand
+// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+#include <Rcpp.h>
+
+using namespace Rcpp;
+
+#ifdef RCPP_USE_GLOBAL_ROSTREAM
+Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
+Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
+#endif
+
+// ts_num_individuals_ptr2
+int ts_num_individuals_ptr2(const SEXP ts);
+RcppExport SEXP _RcppTskitTestLinking_ts_num_individuals_ptr2(SEXP tsSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const SEXP >::type ts(tsSEXP);
+    rcpp_result_gen = Rcpp::wrap(ts_num_individuals_ptr2(ts));
+    return rcpp_result_gen;
+END_RCPP
+}
+
+static const R_CallMethodDef CallEntries[] = {
+    {"_RcppTskitTestLinking_ts_num_individuals_ptr2", (DL_FUNC) &_RcppTskitTestLinking_ts_num_individuals_ptr2, 1},
+    {NULL, NULL, 0}
+};
+
+RcppExport void R_init_RcppTskitTestLinking(DllInfo *dll) {
+    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
+    R_useDynamicSymbols(dll, FALSE);
+}
diff --git a/src/test.cpp b/src/test.cpp
@@ -1,4 +1,4 @@
-#include <tskit.h>
+#include <RcppTskit.h>
 // [[Rcpp::depends(RcppTskit)]]
 // [[Rcpp::plugins(RcppTskit)]]
 
@@ -8,11 +8,11 @@
 //' @examples
 //' ts_file <- system.file("examples", "test.trees", package = "RcppTskit")
 //' ts <- RcppTskit::ts_load(ts_file)
-//' RcppTskit::ts$num_individuals()
+//' ts$num_individuals()
 //' ts_num_individuals_ptr2(ts$pointer)
 //' @export
 // [[Rcpp::export]]
 int ts_num_individuals_ptr2(const SEXP ts) {
   RcppTskit_treeseq_xptr ts_xptr(ts);
   return static_cast<int>(tsk_treeseq_get_num_individuals(ts_xptr));
-}
+}
diff --git a/tools/configure.R b/tools/configure.R

Original file line number	Diff line number	Diff line change
`@@ -1,2 +1,2 @@`
`1`	`1`	`YEAR: 2026`
`2`		`-COPYRIGHT HOLDER: RcppTskitTestPkgLinkingTo authors`
	`2`	`+COPYRIGHT HOLDER: Gregor Gorjanc`